Chromosome-Scale Genome Assembly for Soft-Stem Bulrush (Schoenoplectus tabernaemontani) Confirms a Clade-Specific Whole-Genome Duplication in Cyperaceae.

Autor:	Li Y; Huzhou University, Huzhou, China., Ning Y; Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China.; Sichuan Zoige Wetland Ecosystem Research Station, Prefecture of Aba, China., Zheng YC; East China Inventory and Planning Institute, Hangzhou, China., Lou XY; Zhejiang Wanli University, Ningbo, China., Pan Z; Sichuan Academy of Environmental Policy and Planning, Chengdu, China., Dong SB; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
Jazyk:	angličtina
Zdroj:	Genome biology and evolution [Genome Biol Evol] 2024 Jul 03; Vol. 16 (7).
DOI:	10.1093/gbe/evae141
Abstrakt:	Schoenoplectus tabernaemontani (C. C. Gmelin) Palla is a typical macrophyte in diverse wetland ecosystems. This species holds great potential in decontamination applications and carbon sequestration. Previous studies have shown that this species may have experienced recent polyploidization. This would make S. tabernaemontani a unique model to study the processes and consequences of whole-genome duplications in the context of the well-documented holocentric chromosomes and dysploidy events in Cyperaceae. However, the inference was not completely solid because it lacked homology information that is essential to ascertain polyploidy. We present here the first chromosome-level genome assembly for S. tabernaemontani. By combining Oxford Nanopore Technologies (ONT) long reads and Illumina short reads, plus chromatin conformation via the Hi-C method, we assembled a genome spanning 507.96 Mb, with 99.43% of Hi-C data accurately mapped to the assembly. The assembly contig N50 value was 3.62 Mb. The overall BUSCO score was 94.40%. About 68.94% of the genome was comprised of repetitive elements. A total of 36,994 protein-coding genes were predicted and annotated. Long terminal repeat retrotransposons accounted for ∼26.99% of the genome, surpassing the content observed in most sequenced Cyperid genomes. Our well-supported haploid assembly comprised 21 pseudochromosomes, each harboring putative holocentric centromeres. Our findings corroborated a karyotype of 2n = 2X = 42. We also confirmed a recent whole-genome duplication occurring after the divergence between Schoenoplecteae and Bolboschoeneae. Our genome assembly expands the scope of sequenced genomes within the Cyperaceae family, encompassing the fifth genus. It also provides research resources on Cyperid evolution and wetland conservation. (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
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